Sodium in PDB 7q1d: Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B

All present enzymatic activity of Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B:
2.3.1.81;

The structure of Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B, PDB code: 7q1d was solved by N.Pontillo, A.Guskov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.15 / 1.43
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	90.957, 100.489, 131.908, 90, 90, 90
R / Rfree (%)	17.6 / 20

The structure of Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B (pdb code 7q1d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B, PDB code: 7q1d:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:49.5 occ:1.00 OD1 A:ASP73 2.5 33.8 1.0 O A:HOH624 2.8 40.7 1.0 O A:HOH575 3.0 32.4 1.0 CG A:ASP73 3.6 32.4 1.0 CA A:ASP73 3.8 20.8 1.0 O A:HOH600 3.8 44.6 1.0 O A:MET72 4.1 23.0 1.0 CD A:PRO77 4.2 31.3 1.0 CB A:ASP73 4.2 23.3 1.0 NE2 A:GLN69 4.2 29.4 1.0 N A:ASP73 4.3 21.9 1.0 C A:MET72 4.5 22.8 1.0 OD2 A:ASP73 4.6 32.2 1.0 CG A:PRO77 4.6 35.9 1.0 CA A:THR76 4.8 26.9 1.0 C A:ASP73 4.9 23.0 1.0 O A:ASP73 4.9 23.9 1.0 N A:PRO77 4.9 28.9 1.0

Sodium binding site 2 out of 3 in the Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:45.8 occ:1.00 OE1 A:GLU179 2.2 41.2 1.0 O D:HOH556 2.4 29.1 1.0 CD A:GLU179 3.0 33.1 1.0 O A:HOH485 3.4 33.2 1.0 CB A:GLU179 3.5 25.0 1.0 CG A:GLU179 3.8 24.6 1.0 OE2 A:GLU179 3.8 36.7 1.0 CB D:ALA154 4.0 19.1 1.0 O D:ARG151 4.3 21.8 1.0 CE1 D:HIS137 4.3 22.9 1.0 NE2 D:HIS137 4.4 27.2 1.0 O D:HOH551 4.4 24.4 1.0 O A:HOH610 4.6 46.2 1.0 N D:ALA154 4.8 19.2 1.0 O A:HOH621 4.8 26.0 1.0 O D:GLY150 4.8 20.1 1.0 CA A:GLU179 4.9 19.8 1.0

Sodium binding site 3 out of 3 in the Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Acetyltrasferase(3) Type Iiia in Complex with 3-N-Methyl-Nemycin B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:39.9 occ:1.00 O A:HOH475 2.3 35.8 1.0 OE2 A:GLU179 2.6 36.7 1.0 O A:HOH418 3.1 27.7 1.0 CD A:GLU179 3.5 33.1 1.0 O D:HOH658 3.6 40.6 1.0 CG A:GLU179 3.7 24.6 1.0 CD2 D:HIS137 3.8 25.3 1.0 NE2 D:HIS137 3.9 27.2 1.0 CG A:GLN270 4.2 32.5 1.0 CB D:ALA154 4.4 19.1 1.0 O A:HOH670 4.4 33.3 1.0 O A:ALA177 4.6 21.1 1.0 O A:VAL176 4.6 19.6 1.0 OE1 A:GLU179 4.7 41.2 1.0 O D:HOH446 4.8 26.5 1.0 O D:HOH678 5.0 42.8 1.0

N.Pontillo, E.M.Warszawik, M.Partipilo, A.Stetsenko, M.Loznik, X.Yang, D.J.Slotboom, A.Guskov, A.Herrmann. 3-N-Alkylation in Aminoglycoside Antibiotic Neomycin B Overcomes Bacterial Resistance Mediated By Acetyltransferase (3) Iiia To Be Published.